It appears that you are using Skyline version 21.2.
The current version of Skyline is 23.1.
We usually recommend that you use the latest version of Skyline unless you are trying to reproduce results from older experiments.

We have fixed some bugs in older versions of Skyline which were causing problems when the .skyd file (the file which contains extracted chromatograms) became very large.
It is likely that Skyline 23.1 will have fixed the problems that you are running into.

If you are still having problems with Skyline 23.1, then it would be helpful if you could send us your Skyline document and some of your raw files.
The usual way to send a Skyline document is to use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. It will probably be much larger than that so you would need to upload it here:
https://skyline.ms/files.url

It would also be helpful if you could send us some of your .raw files that you are trying to extract chromatograms from.

However, it is very likely that the problems you are running into will be fixed if you use Skyline 23.1 or Skyline-daily instead of Skyline 21.2.
-- Nick

Hi Nick,

Yes, our skyline version is 21.2. Will all our previous spectral libraries that was build during version 21.2 be affected if we upgrade to version 23.1? Eg. having to redo iRT databases/unable to open skyline files. Is there anyone who encounter this before as we are worried that we won't be able to open the files or having to redo all the settings.

Additionally, is it possible to extract the signal-to-noise ratio for each peak integration in skyline?

Thank you for the help!

Yes, everything will work great when you switch to using the newer version of Skyline.
Newer versions of Skyline are always able to read documents produced by older versions of Skyline.
If you ever need to go the other way, and produce a document which can be read by an older version of Skyline you can use the "File > Share" menu item and then choose the older version of Skyline to target in the Share Document dialog.

By the way, if you ever need to install an older version of Skyline on your computer, you can find links to older versions from the "Unplugged" installer page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-64-disconnected_23_1
After you click the "Accept" button an "archive" link will appear that will take you to a page where you can download all older versions of Skyline.
-- Nick